Antibiotic-resistant superbug arose in northern Manhattan

Its spread is happening not through hospitals but through households.

Human skin is a garden of microbes that is home to about 1,000 bacterial species. Most are benign, but some invade the skin and cause illness—of these, antibiotic-resistant bacteria are particularly dangerous.

We normally associate these resistant bugs with hospitals, but new research finds that they could be living and spreading in households and within communities, too. For one notoriously resistant bug, scientists have also been able to pinpoint where and when it first began spreading. The hope is that this knowledge will allow a better way of controlling infection and stopping epidemics.

The Staph of nightmares

About one in five humans carries the disease-causing bacteria Staphylococcus aureus, or Staph, on their skin without any problem. However, breached skin, surgical wounds, or low immunity (often caused by HIV infection or cancer treatments) may allow Staph to cause diseases ranging from minor skin ailments to catastrophic infections.

The spread of methicillin-resistant Staphylococcus aureus (MRSA) is well known. Originally associated with infections in hospitals and nursing homes, MRSA is now known to colonize the skin of otherwise healthy individuals—these infections are called "community-associated" (CA-MRSA).

CA-MRSA spreads by contact with an infected individual. That's why the spread of CA-MRSA can occur in households, where the contact between house members is difficult to control. This also results in high rates of recurrent infection due to contaminated household objects such as shared razors, towels, and door knobs.

Global epidemic

While the presence of Staph on skin has always put people at risk for infection, two features make CA-MRSA riskier. It can cause severe disease in previously healthy people. In about one in every ten cases, CA-MRSA infections lead to deadly pneumonia, severe sepsis, or the dreaded "flesh-eating disease" (aka necrotizing fasciitis). They also have the ability to spread rapidly, which has helped propel them to a global epidemic.

The global epidemic has been attributed to a single CA-MRSA microbe known as USA300. In the US, it is responsible for outbreaks in 38 states, and it has spread to Canada and several European countries. Studies of USA300 have found molecular evidence that suggests it has the ability to readily evolve into more harmful versions.

USA300’s invasion of community households is less well understood. To change that, Anne-Catrin Uhlemann at Columbia University Medical Center and her colleagues have used whole-genome sequencing to reconstruct USA300’s evolutionary history. The results have been published in PNAS.

Whole-genome sequencing takes a snapshot of an organism’s complete genetic makeup. Uhlemann obtained Staph cells from 161 CA-MRSA-infected residents in New York City and combined their genome data with health statistics to gain insights into USA300’s spread during a period covering 2009-2011.

They looked for small changes in the genome, which often give clues about how the cell evolved. After investigating more than 12,000 small changes in the USA300 genome, the authors reconstructed its genetic history. This helped them determine that USA300 first arose around 1993. The molecular signatures allowed them to also home in on the geographic location where this happened, which they determined to be right in Columbia’s neighborhood: northern Manhattan.

Sneaky bug

Detailed study of USA300's genome showed it acquired antibiotic resistant genes from viruses that infect bacteria. The authors also discovered a smaller subgroup of USA300 resistant to another antibiotic class, fluoroquinolones, which appeared to evolve around the time when fluoroquinolone prescription rates had soared in the US.

All this information put together shows that USA300 originally evolved and spread in households and communities in New York City before going global. The occurrence of different antibiotic-resistant bugs highlights the effects of overuse of antibiotics. But working out how CA-MRSA spread within households and inside communities may help researchers devise an infection control strategy that can break this pattern of spread and reduce the possibility of another large-scale outbreak.

Could we please stop prescribing antibiotics for every little cough and sniffle already? These antibiotic resistant diseases are starting to get scary.

Can we also please finish the bottle like the doctor said instead of quitting the minute the symptoms subside? Can we stop saving them for later so we can take one or two the next time we're sick? People do this. Its retarded and potentially dangerous.

Uhlemann obtained Staph cells from 161 CA-MRSA-infected residents in New York City

And shockingly the origin of this microbe turned out to be in New York City. Sampling bias, much?

you missed the rest of the sentence?

Quote:

and combined their genome data with health statistics to gain insights into USA300’s spread during a period covering 2009-2011.

Seems like they took the data, and used it with the rest of the info they have about it.

I did see that. "Health statistics" is not genomic data.

If I take handwriting samples of 161 New Yorkers, then try to match an unknown writing sample to any of 10,000 people worldwide, the only ones I could possibly match are the New Yorkers. It's possible the unknown is sufficiently unlike the New Yorkers' to exclude them, but the only possible match is to a New Yorker.

Don't lose sleep over it anyway. It's like global warming; Human nature forbids us from doing anything about it. Can't be avoided, really. There's no sense in worrying about it. Could be nice to have a convenient and painless exit whenever things get too bad, though. It probably wont happen while we're alive, I hope.

Uhlemann obtained Staph cells from 161 CA-MRSA-infected residents in New York City

And shockingly the origin of this microbe turned out to be in New York City. Sampling bias, much?

Except for the sentence "The global epidemic has been attributed to a single CA-MRSA microbe known as USA300" So they just pulled local variants of a known global version and started tracing the gnome.

Does this mean people will stop blaming antibiotic use on antibiotic resistance when the primary culprit for mutation is virus infections.

It never made sense that antibiotics would be the cause. Most antibiotics never showed signs of causing DNA damage in the bacteria they were affecting, so how could it cause the mutations?

It doesn't cause the resistance, as that was naturally existing in the wild. But it does promote the proliferation of the resistance by eliminating bacteria without the resistance. Also, bacteria can share genomes, so that resistance can spread from one to another, even if the latter never had or needed the resistance.

Does this mean people will stop blaming antibiotic use on antibiotic resistance when the primary culprit for mutation is virus infections.

It never made sense that antibiotics would be the cause. Most antibiotics never showed signs of causing DNA damage in the bacteria they were affecting, so how could it cause the mutations?

That's not how evolution works.

The antibiotic misuse wipes out most of the weak bacteria. The ones left are "lucky" - either because they were hanging out in some tissue that got a lower dose (etc) or because they have a gene that helps a little bit versus antibiotics - maybe a cell-surface pump that secretes who-knows-what but also secretes the antibiotic molecules when they pass on by. With each wave of antibiotic exposure, the few survivors are disproportionately the ones with the (low efficiency) antibiotic exporter, or degrader, or whatever-er gene. As time goes on, that gene mutates as normal and eventually a mutation or 10 occur which makes it much better at pumping antibiotics out of the cell.

Once it's real good at that, it's a huge survival advantage in bacteria that tend to get nuked with antibiotics, and it spreads rapidly. Then, it spreads between species via bacterial conjugation, and via bacteriophages (viruses) which slurp up a copy of the resistance gene instead of a copy of the viral DNA (viruses are actually in many cases mostly malformed, since portions of the assembly process are often stochastically 'random'). The virus body then happily injects this DNA into a completely different cell, quite possibly even species, and it may get incorporated into the host genome or a plasmid using the virus's other proteins which are designed to do just that.

Viruses can and do cause mutations, but they're almost certainly not the primary source of antibiotic resistance, just a transfer vector.

Do people really share razors? That seems even worse than toothbrushes!

I had to read that twice myself, but :

"This also results in high rates of recurrent infection"

Recurrent infection is the key, I think the idea is you re-infect yourself (that is, you are infected, shave, beat the infection, shave, and re-infect). Seems that CA-MRSA is not only antibiotic resistant, but antibody as well

It's times like this when I wish the Creationists were right and Evolution wasn't true. Stuff like MRSA couldn't evolve in their world and wouldn't be killing people.

VRSA is expected to spread over the next few years, and while vancomycin does still work against MRSA (but not as good as methicillin worked against PRSA), it doesn't against VRSA. We've got nothing against it.

I think it sort of caters to this myth that there are just a few bacteria here and there that can make you sick, and you can wipe them out by buying and applying the correct consumerist BS. No. There are trillions and trillions and trillions of bacteria everywhere. Everything you see is covered in them, including you. COVERED. That "kills 99.9% of germs!" statement, when applied to a single square foot of countertop, probably still leaves a few tens of millions of bacteria on the countertop after the antibacterial crap gets wiped over it.

There are ten times as many bacterial cells in a human body as there are human cells. People aren't very good at imagining big numbers and teeny things, but maybe that factoid could bring it into context.

Triclosan, which is in a lot of hand soaps, is also questionable both in its safety at the rates it's being dumped down the drain, and basically does nothing other than promote triclosan resistance because if you're trying to use it right, you should be washing your hands for about a minute. Again, pre-surgery, sounds about right. Nobody does that, so it's utterly pointless.

This is a very visible part of the problem. An anti-bacterial agent that is 99% effective leaves 1% survivors which are heavily biased towards resistance to the anti-bacterial.

Uhh dude, you do understand those aren't the same type of "antibiotic", right? Resistance to bleach doesn't , in any way, equal resistance amoxicillin.

When we run out of triclosan-susceptible bacteria, and it's time for your surgery, you're gonna have a bad time.

I suppose any application that needs to be as bacteria-free as possible could fall back to being autoclaved or soaked in alcohol. Except those applications for which that won't work.

That wasn't the point - we're talking antibiotic resistant vs antibacterial. The method of killing the little buggers is quite different between the two, so one's resistance wouldn't have any direct effect on the other. You're triloscan superbug could still be taken care of by antibiotics.

I agree, it's a scary situation if you had a bug that's resistant to antibiotics and antibacterial soaps. But we still shouldn't confuse the two

Does this mean people will stop blaming antibiotic use on antibiotic resistance when the primary culprit for mutation is virus infections.

It never made sense that antibiotics would be the cause. Most antibiotics never showed signs of causing DNA damage in the bacteria they were affecting, so how could it cause the mutations?

It doesn't cause the resistance, as that was naturally existing in the wild. But it does promote the proliferation of the resistance by eliminating bacteria without the resistance. Also, bacteria can share genomes, so that resistance can spread from one to another, even if the latter never had or needed the resistance.

No, it actually doesn't and this is a common misconception being repeatedly constantly that makes absolutely no sense if you grasp how truly diverse bacteria is in the wild. (There are millions if not billions of unique types of bacteria all clumped in to huge, assumed to be similar groups.)

The majority of bacteria work together in some way, in little ecosystems, where one species might break down a particular element so another species can eat and vice versa.

Many antibiotics kill off a particular one of those bacteria in the tiny ecosystems, so the others die or go dormant, but it doesn't always actually kill the bacteria causing the problem most of the time. The deadly bacteria can still persist but in a muted state or stasis waiting for the ecosystem to revive.

When a new neighbor arrives that can fill the place of the killed off species, the process renews.

So, evolutionary pressure isn't the issue in the majority, it's the ecosystem. When a virus invades the ecosystem, it can alter it and it has always been the primary driving force for drug resistance.

This is a very visible part of the problem. An anti-bacterial agent that is 99% effective leaves 1% survivors which are heavily biased towards resistance to the anti-bacterial.

Uhh dude, you do understand those aren't the same type of "antibiotic", right? Resistance to bleach doesn't , in any way, equal resistance amoxicillin.

When we run out of triclosan-susceptible bacteria, and it's time for your surgery, you're gonna have a bad time.

I suppose any application that needs to be as bacteria-free as possible could fall back to being autoclaved or soaked in alcohol. Except those applications for which that won't work.

That wasn't the point - we're talking antibiotic resistant vs antibacterial. The method of killing the little buggers is quite different between the two, so one's resistance wouldn't have any direct effect on the other. You're triloscan superbug could still be taken care of by antibiotics.

I agree, it's a scary situation if you had a bug that's resistant to antibiotics and antibacterial soaps. But we still shouldn't confuse the two

Anti-bacterial soaps are anti-bacterial due to the inclusion of an anti-biotic. Every anti-biotic that is used to train bacterial resistance is one less that can be used as an anti-biotic. To be effective, they require a population that is not composed of those that survived exposure to the anti-biotic.

Penicillin was the wonder drug. It was so wonderful that it was used everywhere. Penicillin is now a minor drug. It was so wonderful that penicillin resistance is favored even if it has a survival cost. This is being repeated with each of the useful antibiotics. Wow it works, lets use it as widely as possible and make sure the entire bacterial population is able to live with it!

Triclosan is a useful antibiotic. That usefulness will end soon due to the popularity of triclosan infused cleansers that are not 100% effective. Natural selection favors those not killed. Those not killed are more likely to be resistant, raising the percentage of survivors in the next round until the "effectiveness" drops to the point where the FDA demands a change in labeling due to lack of effectiveness and side effects.

Could we please stop prescribing antibiotics for every little cough and sniffle already? These antibiotic resistant diseases are starting to get scary.

It's not just an over prescription problem. Of equal importance is patients finishing treatment with their prescribed medication. When people stop taking their medication mid-cycle - usually because they feel better - it allows whatever bacteria remains in the system to propagate and flourish. There needs to be more education on both sides of this issue.

Even though Triclosan is an antibacterial instead of a antibiotic, I'm just going to toss it out there that scientists are starting to figure out just how bad it is for us. As in a single "normal" dose can inhibit muscle contraction by as much as 40%, and it is absorbed through the skin.

I have RSI injuries in my hands due to computer use, and one of the things I've had to do is eliminate triclosan containing soaps. I have my own small container of normal soap that I have to carry around with me at work. It does seem to make a difference. If I use the soap stocked in the bathrooms for a few days, my hands get noticeably worse, even if I continue my stretching and exercising routines as normal.

Back on topic, I think doctors are a bit better than they used to be about educating people, but it's been a hard fight. I recently had to take my 8 month old in for croup and my mother-in-law was insisting they should give her some antibiotics. Fortunately, my wife is a biologist and set her straight.

What I've always wondered about are the antibacterial hand sanitizers. I know a hospital grade 90% alcohol rub is effective vs viruses, but are consumer grade (usually 63% or less)? The people I know treat it as though it were divinely gifted at killing anything not human flesh, but I have to cringe when people hold out their hands for my daughter and utter the words "I used hand sanitizer!", and the bottle says "antibacterial hand gel."

I can't help but have some small part of me wishing I could tell them to go wash their hands without horribly offending people. The alcohol rubs in the hospital? Yeah, definitely a good idea, and it is far better than soap in those strengths. Not so sure on the Kmart variety, here.

I recently had a bad cold for about 2 weeks. I felt pretty miserable, but whatever. I had dozens of people at work (I was not allowed to take more than 2 days off) tell me to go to the doctor and get antibiotics.... FOR A COLD?!?!?!? My response to them, was "I don't believe in taking antibiotics unless I am in danger of death. I see it as my way of helping to save the human race and the collapse of our society" Their response to me. "yeah, but you will feel better".

This will fall on the medical community 100%. When a patient comes in, no matter how much they BITCH... Don't give them antibiotics unless they are literally going to die.

Reminds me of a girl at work, not the brightest person, who stopped taking her antibiotics because she "started feeling better." Then she'd get sick again and go back to the doctor to get the same antibiotics and would repeat the cycle. I told her she'd end up killing us all by making superbugs.

Uhlemann obtained Staph cells from 161 CA-MRSA-infected residents in New York City

And shockingly the origin of this microbe turned out to be in New York City. Sampling bias, much?

Except for the sentence "The global epidemic has been attributed to a single CA-MRSA microbe known as USA300" So they just pulled local variants of a known global version and started tracing the gnome.

Maybe there was some prior knowledge that it originated in New York. But then discovering that it originated in New York isn't a contribution. Pinpointing to 1993 is kinda interesting.

Do we know the rough date of emergence? There were three different Surgeons General that year, and I want to know who to blame

Could we please stop prescribing antibiotics for every little cough and sniffle already? These antibiotic resistant diseases are starting to get scary.

I cant remember the last time my son got antibiotics for a cough or sniffle. Then again i dont bring him in for every little cough of sniffle.

Well, there are parents that demand antibiotics for everything. For themselves AND their children. Most of them pester the doctor until they get them, even if it is the flu or a cold. And some doctors probably give in just to get them out of the way.

Pair that up with all the dolts who use triclosan in every single product out there and we're just making it worse.

Does this mean people will stop blaming antibiotic use on antibiotic resistance when the primary culprit for mutation is virus infections.

It never made sense that antibiotics would be the cause. Most antibiotics never showed signs of causing DNA damage in the bacteria they were affecting, so how could it cause the mutations?

It doesn't cause the resistance, as that was naturally existing in the wild. But it does promote the proliferation of the resistance by eliminating bacteria without the resistance. Also, bacteria can share genomes, so that resistance can spread from one to another, even if the latter never had or needed the resistance.

No, it actually doesn't and this is a common misconception being repeatedly constantly that makes absolutely no sense if you grasp how truly diverse bacteria is in the wild. (There are millions if not billions of unique types of bacteria all clumped in to huge, assumed to be similar groups.)

The majority of bacteria work together in some way, in little ecosystems, where one species might break down a particular element so another species can eat and vice versa.

Many antibiotics kill off a particular one of those bacteria in the tiny ecosystems, so the others die or go dormant, but it doesn't always actually kill the bacteria causing the problem most of the time. The deadly bacteria can still persist but in a muted state or stasis waiting for the ecosystem to revive.

When a new neighbor arrives that can fill the place of the killed off species, the process renews.

So, evolutionary pressure isn't the issue in the majority, it's the ecosystem. When a virus invades the ecosystem, it can alter it and it has always been the primary driving force for drug resistance.

I've always had the impression that the microscopic world was a perpetual World War, where everyone is at war with everyone else, except for those few slime molds and slime bacteria colonies, which are, I believe, in the vast minority in the microscopic world.

Regardless, even in basic biology classes in college, we trained bacterial resistance as a lab experiment, where we would gradually increase the antibiotic present. Each successive increase would decrease population initially, but the bacterial colonies would recover. In the end, we had bacteria that could survive a high dosage of antibiotics. The control for this experiment was an agar dish of the "same" (as close as you can get in a lab class at any rate) bacteria, which we gave the final dose of antibiotic at the beginning. The control dish was completely empty, even days after the experiment.

And every group in the lab got the same result. High dosage immediately: complete wipeout. Gradually increasing dosage to the same level as the control received: surviving colonies.

So I would submit to you that viruses may vary well be the primary cause of gene transmission (I honestly don't know), but I don't believe that viruses are the primary cause of antibiotic resistance. Why would they be? Now, if antibiotic resistant strain becomes dominant in an area, then it is entirely reasonable to think that there becomes an orders of magnitude higher probability that a virus will be able to transmit that gene to other strains elsewhere, but the virus isn't producing the antibiotic, and without antibiotic in the environment, it seems reasonable that bacteria would lose the gene as that precious space on their genome would be better served by other genes that do confer a survival advantage.

Even though Triclosan is an antibacterial instead of a antibiotic, I'm just going to toss it out there that scientists are starting to figure out just how bad it is for us. As in a single "normal" dose can inhibit muscle contraction by as much as 40%, and it is absorbed through the skin.

I have RSI injuries in my hands due to computer use, and one of the things I've had to do is eliminate triclosan containing soaps. I have my own small container of normal soap that I have to carry around with me at work. It does seem to make a difference. If I use the soap stocked in the bathrooms for a few days, my hands get noticeably worse, even if I continue my stretching and exercising routines as normal.

Back on topic, I think doctors are a bit better than they used to be about educating people, but it's been a hard fight. I recently had to take my 8 month old in for croup and my mother-in-law was insisting they should give her some antibiotics. Fortunately, my wife is a biologist and set her straight.

What I've always wondered about are the antibacterial hand sanitizers. I know a hospital grade 90% alcohol rub is effective vs viruses, but are consumer grade (usually 63% or less)? The people I know treat it as though it were divinely gifted at killing anything not human flesh, but I have to cringe when people hold out their hands for my daughter and utter the words "I used hand sanitizer!", and the bottle says "antibacterial hand gel."

I can't help but have some small part of me wishing I could tell them to go wash their hands without horribly offending people. The alcohol rubs in the hospital? Yeah, definitely a good idea, and it is far better than soap in those strengths. Not so sure on the Kmart variety, here.

Anti-bacterials are antibiotics. The difference in products labeled with these terms is that antibiotics are safe to eat or inject. Antibacterials are topical. That is they are applied to the skin and may exhibit anti-human effects if taken internally.

Biotic==life form. Anti-Biotic==life form killer. Arsenic is a very effective antibiotic. Not recommended for internal use by humans though due to its effectiveness as a general purpose antibiotic. The preferred antibiotics for humans are safe for internal use-antibacterials with a very few targeting parasites. Generally though, those that are not antibacterial are not labeled antibiotic. A number of new cancer treatments are more general antibiotics designed to kill aberrant human tissues. While antibiotic in effect, they are generally referred to as chemotherapies instead.

Medical antibiotics are safe for the (majority) patient population to use internally.Medical antibacterials may be unsafe for consumption and should be not be taken internally.

When medicines called antibiotics start targeting viruses and non-bacterial parasites then the difference in terms will become meaningful in terms of the target illness. For now the difference between antibiotic and antibacterial is safe/unsafe for internal use. Both are antibacterial until the bacteria gain resistance, in which case the side effects on human health become the dominant effect.

Alcohol is not the magic bullet it is always assumed to be. There are a number of toxic bacteria that are alcohol tolerant. It is useful though in that it is an effective cleanser and does kill off the majority of toxic bacteria and viruses when used correctly. Blending in a second chemical that kills off alcohol tolerant organisms makes for a very effective topical disinfectant. The problem being that extremely effective disinfectants commonly are wide spectrum antibiotics making them unsafe for human and pet consumption.

MRSA and VRSA can easily be killed off by common disinfectants. The problem comes when it is time to treat a patient as those common disinfectants are broad spectrum antibiotics that include animals (including humans) in the class of biotics they will eliminate. Topical use only and even then, some of these treatments will destroy skin and fur.

The Conversation / The Conversation is an independent source of news and views, sourced from the academic and research community. Our team of editors work with these experts to share their knowledge with the wider public. Our aim is to allow for better understanding of current affairs and complex issues, and hopefully improve the quality of public discourse on them.